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[ADAM-1992] Make maximum FASTQ read length configurable. #2011

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@fnothaft
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@fnothaft fnothaft commented Jul 6, 2018

Resolves #1992.

@fnothaft fnothaft added this to the 0.24.1 milestone Jul 6, 2018
@fnothaft fnothaft requested a review from heuermh Jul 6, 2018
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@coveralls coveralls commented Jul 6, 2018

Coverage Status

Coverage remained the same at 78.933% when pulling cf1204d on fnothaft:issues/1992-fastq-10000bp into 8e8007e on bigdatagenomics:master.

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@coveralls coveralls commented Jul 6, 2018

Coverage Status

Coverage remained the same at 78.933% when pulling cf1204d on fnothaft:issues/1992-fastq-10000bp into 8e8007e on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Jul 6, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2782/
Test PASSed.

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@heuermh heuermh left a comment

Minor code style suggestions

@@ -60,6 +60,13 @@
* application. We'll see if someone complains in other applications.
*/

public static final String MAX_READ_LENGTH_PROPERTY = "org.bdgenomics.adam.io.FastqRecordReader.MAX_READ_LENGTH";

public static void setMaxReadLength(Configuration conf,

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heuermh Jul 7, 2018
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Code style: add javadocs, make parameters final

@@ -60,6 +60,13 @@
* application. We'll see if someone complains in other applications.
*/

public static final String MAX_READ_LENGTH_PROPERTY = "org.bdgenomics.adam.io.FastqRecordReader.MAX_READ_LENGTH";

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@heuermh

heuermh Jul 7, 2018
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add

public static final int DEFAULT_MAX_READ_LENGTH = 10000;
@@ -104,7 +111,7 @@
/**
* Maximum length for a read string.
*/
private static final int MAX_LINE_LENGTH = 10000;
private int MAX_LINE_LENGTH;

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@heuermh

heuermh Jul 7, 2018
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Code style: lower camel case variable name

@@ -135,6 +142,8 @@
*/
protected FastqRecordReader(final Configuration conf,
final FileSplit split) throws IOException {
MAX_LINE_LENGTH = conf.getInt(MAX_READ_LENGTH_PROPERTY, 10000);

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@heuermh

heuermh Jul 7, 2018
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use DEFAULT_MAX_READ_LENGTH above

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@heuermh heuermh commented Nov 5, 2018

Closing in favor of #2077

@heuermh heuermh closed this Nov 5, 2018
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4 participants